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Yorodumi- PDB-1dqh: CRYSTAL STRUCTURE OF HELIX II OF THE X. LAEVIS SOMATIC 5S RRNA WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dqh | ||||||
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Title | CRYSTAL STRUCTURE OF HELIX II OF THE X. LAEVIS SOMATIC 5S RRNA WITH A CYTOSINE BULGE IN TWO CONFORMATIONS | ||||||
Components |
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Keywords | RNA / DOUBLE HELIX / CYTOSINE BULGE | ||||||
Function / homology | RNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Xiong, Y. / Sundaralingam, M. | ||||||
Citation | Journal: RNA / Year: 2000 Title: Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge. Authors: Xiong, Y. / Sundaralingam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dqh.cif.gz | 19.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dqh.ent.gz | 12.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dqh_validation.pdf.gz | 376.2 KB | Display | wwPDB validaton report |
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Full document | 1dqh_full_validation.pdf.gz | 376.2 KB | Display | |
Data in XML | 1dqh_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 1dqh_validation.cif.gz | 4.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dqh ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dqh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 2806.735 Da / Num. of mol.: 1 / Fragment: HELIX II OF 5S RRNA / Source method: obtained synthetically |
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#2: RNA chain | Mass: 3231.988 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.05 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MGCL2, CACL2, CACODYLATE, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 263 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→22.59 Å / Num. all: 6696 / Num. obs: 6070 / % possible obs: 90.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: CNS
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |